I think Game Freak is portraying the legendary Pokémon wrongly.
Legendary Pokémon are a sight to behold. They exist way prior to your arrival to the region and are often deemed as extremely rare. These characteristics tend to be even more extreme in the case of version cover legendaries. For a normal human, seeing a legendary for a brief moment is something that can happen once in a lifetime and only if you are lucky enough. Ho-Oh, for example, had an entire folklore constructed upon centuries of myths regarding its existence.
This empathizes the feeling that, often, legendaries are ancient creatures to some way related to the very essence of the world you are living in. That’s why, while mentioned, you keep asking to yourself: what is Ho-Oh? What is Lugia? Where are they? How are they? What about Groudon, Kyogre, or Rayquaza? What about Mewtwo? This extrange, incredibly powerful creature you find in a remote cave or somewhere else, only after having proved yourself as worthy upon player progression. And although you've already been inevitably spoiled in the cover art of the Pokémon box, you still have plenty of doubts concerning the specifics of your first meeting.
The fact that the legend of the legendary is unrelated to you in the big picture also helps when it comes to distinguish them. You are nobody. A dude that happens to be in the right place at the right time, fighting something greater than him. The main legendary is not just another ‘mon in your team, is a game accomplishment, a ‘mon that lends you its exceptional power as an extremely rare gift.
I loved when the latitwins were roamers. They had 0 relation with the main character; Pokémon of legend, as they say. You were having fun and then oh shit, it’s Lati@s, as your heart suddenly accelerated with excitement, knowing it could be the last time you saw it for a long time. In Pokémon Emerald, something similar happens. When you reach Sky Pillar in order to ask for Rayquaza’s help, you don’t even stablish interaction with it; it just flies immediately to fulfill its duty, leaving you watching.
Now, in this games I think that, again, we are too much of the protagonist here. One thing is that, from a playable perspective, you are able to show any Pokémon you have to players online. It’s the same thing when you engage in a trade or a battle; it doesn’t matter if you have 3 boxes of Shiny Groudon, this is for the sake of the playable environment. But one thing completely different is when that vision infects the main story of the game. To me, it seems ridiculous that a guy is, from the get go to make things worse, riding a legendary Pokémon through the entirety of a region, a region in which they are probably considered saviors, heroes, tale legends or representatives of some sort. “Ey, look at that guy traveling in Miraidon”.
It’s like… no? When you get to fight Ho-Oh, you know you are in the mid of an exceptional event. In fact, almost no one knows about your battle against it. What am I saying? No one apart from the kimono girls and the sages is even sure of its existence at this point, most have already mixed legend with reality. This doesn’t happen in the games because they don’t reinforce the narrative to this extent, but you know, you sure KNOW, that if you were to use that Ho-Oh in battle against an NPC, that NPC would be left speechless either asking himself what Pokémon is that or trying to accept that what their eyes are seeing is the truth, because in the context of the Pokémon world it would’ve similar, and I’m not exaggerating, to suddenly see Christ nice and clear.
So, why don’t the guy start as a no-name, a random with a Weedle that eventually has things his way, and instead feels like a privileged boy with access to a creature of legend from the very beginning. I don’t really like what it conveys.